4JRW
Crystal structure of Clostridium histolyticum colg collagenase PKD domain 2 at 1.6 Angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2C4X |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.95 | α = 90 |
b = 48.992 | β = 90 |
c = 70.858 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 113 | CCD | RIGAKU SATURN 92 | 2008-04-05 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 93 | CCD | ADSC QUANTUM 315 | 2008-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5478 | ||
2 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.919457 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1,2 | 1.6 | 37.9 | 99.9 | 0.061 | 30.9 | 4.1 | 39924 | 39884 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2 | 1.58 | 1.69 | 99.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2C4X | 1.6 | 37.9 | 20556 | 20159 | 1092 | 99.9 | 0.1782 | 0.17649 | 0.20951 | RANDOM | 20.237 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.49 | -0.29 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.237 |
r_dihedral_angle_4_deg | 21.012 |
r_dihedral_angle_3_deg | 15.157 |
r_scangle_it | 6.166 |
r_dihedral_angle_1_deg | 5.557 |
r_scbond_it | 3.795 |
r_mcangle_it | 2.492 |
r_angle_refined_deg | 2.042 |
r_mcbond_it | 1.479 |
r_chiral_restr | 0.166 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1290 |
Nucleic Acid Atoms | |
Solvent Atoms | 209 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
PHASER | phasing |
CCP4 | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
CCP4 | phasing |